The Bioscreencast Blog

One of our motivations for starting bioscreencast.com was the rather poor resolution of screencasts hosted on youtube. Most screencasts on youtube suffer due to the high degree of compression youtube puts its videos through. Screencasts generally convey a lot more when you can actually read and see whats going on on the screen.The fine text, the snazzy antialiased icons , all suffer at the hands of most compression settings , making it rather painful to follow along.

However , youtube recently added a feature that may offer a small way out of this, especially for screencasts. Youtube annotations. What this basically allows you to do is add small text pop-ups on the videos you author ( kinda like VH1s popup video) .

The popups can be finely controlled down to the tenths of a second for appearance and dissaperance and come in three flavors , text box , speech bubble and spotlights. I first heard about this feature on Jon Udells blog where he talks about how this really adds value to screencasts and couldnt wait to try the feature out . I went all out and edited one of my bioscreencast screencasts which explain how to use the “links popup” and “History option” to combine searches on the NCBI for biomedical search and put it up on youtube. Since the youtube embed player still does not support these annotations , check out the video on the youtube site itself by clicking on this link.

Having switched to using a mac almost a year and a half back. I generally keep track of screencasting apps for the mac. The unofficial apple weblog (tuaw) has a very good review of screencasting apps for the Mac. Check out the review and let us know which apps you prefer by writing in or better yet,  put it up on our Mac screencast wiki page.

I personally have always used IShowU  for capture and  Quicktime-Pro for all my editing, but with the entry of all these options maybe I will check some of  these out.

-hari

Michael Pascoe is back and his latest screencast tells you how to use the equation editor in Microsoft Word, something all of us have struggled with in our lives, especially if you have a paper to submit for class.

Watch away (best way to watch is to expand the video to full size)

Technorati Tags: screencast, equations

Neuroscience is a fascinating subject for many, and for various reasons, I have a rather soft spot for the field. The computational challenges of neuroscience are, surprise surprise, rather intriguing. After all, our brain is in many ways the ultimate computer, and we are always trying to figure out how it works and how to replicate intelligence artificially.

Through Frank Gibson’s screencasts on Bioscreencast, I found out about the CARMEN, a neuroinformatics project that aims to “create an e-science infrastructure in which data on neuronal activity (electrical and optical measures) can be shared, stored, manipulated and modelled”.

Neuroinformatics is data intensive and is fed by heteregenous data types. Unfortunately a lot of the data is confined to a single lab, i.e. the broader community is not being tapped properly (something that was forced onto biology by the sheer breadth of the human genome project). But the CARMEN project leapfrogs some of the trajectory of bioinformatics, by providing a virtual laboratory that incorporates knowledge about experimental conditions and extensive amounts of meta-data. It took biofinformaticians a long time to realize that capturing experimental information as meta-data was important.

CARMEN is an ambitious project, and to be truly successful will need to last a lot longer than the current 4 year pilot.

This presentation tells you about the CARMEN project, and some of the challenges the project hopes to address.

Back when we thought about putting Bioscreencast together, we had a vision of people doing their daily work, realizing that there was something interesting to share, turning on their favorite screencasting app, and then recording a screencast. Today, Michael Pascoe uploaded a screencast that, for me, personifies that vision. In the screencast below, Michael demonstrates how he uses Illiad and Papers to pursue a paperless PhD (If you have a Mac and $42 you HAVE to get this). The screencast is short, it’s simple, and it makes you want to go and get Papers. Perfect!!!

Technorati Tags: Illiad, Library, Papers

How often have you heard someone say ” I dont know how you look for something in there” . Database querying and search has become an essential skill to possess in this genomic age.  Be it PUBMED , FlyBase or the PDB, we all rely on these databases to find our everyday information.

As Jon Udell commented in  his article on search strategies, database querying is definitely a skill , and good searchers tend to have deep and hidden reservoirs of tacit skill that they can harness . And, as he says , like many other skills effective search can be learned.

We at Bioscreencast.com believe that screencasts are a good way to capture user-database interactions . It was for this reason that we decided to have a category in our library called “Databases and Biosearch”.  Thanks to uploads like the recent one from the PDB , we have user uploaded screencasts that show you how to search databases, ranging from the new Uniprot database , the gaggle proteomics workbench to the Membrane Protein databank .

We hope that the next time you hit on a clever querying strategy  or put together a public database, you screencast it for us all to benefit from.